Abstract
High-quality molecular markers are essential for marker-assisted selection to accelerate breeding progress. Compared with diploid species, recently diverged polyploid crop species tend to have highly similar homeologous subgenomes, which is expected to limit the development of broadly applicable locus-specific single-nucleotide polymorphism (SNP) assays. Furthermore, it is particularly challenging to make genome-wide marker sets for species that lack a reference genome. Here, we report the development of a genome-wide set of kompetitive allele specific PCR (KASP) markers for marker-assisted recurrent selection (MARS) in the tetraploid minor crop perilla. To find locus-specific SNP markers across the perilla genome, we used genotyping-by-sequencing (GBS) to construct linkage maps of two F2 populations. The two resulting high-resolution linkage maps comprised 2326 and 2454 SNP markers that spanned a total genetic distance of 2133 cM across 16 linkage groups and 2169 cM across 21 linkage groups, respectively. We then obtained a final genetic map consisting of 22 linkage groups with 1123 common markers from the two genetic maps. We selected 96 genome-wide markers for MARS and confirmed the accuracy of markers in the two F2 populations using a high-throughput Fluidigm system. We confirmed that 91.8% of the SNP genotyping results from the Fluidigm assay were the same as the results obtained through GBS. These results provide a foundation for marker-assisted backcrossing and the development of new varieties of perilla.
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Data availability
The datasets generated during and/or analysed during the current study are available in the NABIC (National Agricultural Biotechnology Information Center, https://nabic.rda.go.kr/) repository, [NN-5662 ~ 5712].
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This work was supported by a grant from the National Agricultural Genome Project (No. PJ013355032021), Rural Development Administration, Republic of Korea.
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JO, JE, SH, and JH conceived and designed the experiments; JO and JE conducted the SNP analysis, linkage map construction, and data analysis; JK constructed the GBS library; MH developed the mapping population; TH provided the draft genome; KL participated in discussions about the experiments; SH and JH wrote and reviewed the manuscript.
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Oh, JE., Kim, JE., Kim, J. et al. Development of an SNP marker set for marker-assisted backcrossing using genotyping-by-sequencing in tetraploid perilla. Mol Genet Genomics 298, 1435–1447 (2023). https://doi.org/10.1007/s00438-023-02066-6
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DOI: https://doi.org/10.1007/s00438-023-02066-6